Biology subjects

Chen, L.

Publications and source records attributed to Chen, L..

At least 973 records · Page 54Linked to original sources

bioRxiv2019

Quantifying the impact of genetically regulated expression on complex traits and diseases

About 90% of risk variants identified from genome-wide association studies (GWAS) are located in non-coding regions, highlighting the regulatory role of genetic variants. We propose a unified statistical framework, IGREX, for quantifying the impact of genetically regulated expression (GREX). This is achieved by estimating proportion of phenotypic variations that can be explained by the GREX component. IGREX only requires summary-level GWAS data and a gene expression reference panel as input. In real data analysis, using 48 tissues from the GTEx project as the reference panel, we applied IGREX to a wide spectrum of phenotypes in GWAS, and observed a significant proportion of phenotypic variations could be attributed to the GREX component. In particular, the results given by IGREX revealed tissue-across and tissue-specific patterns of the GREX effects. We also observed strong association between GREX effect and immune-related proteins, further supporting the relevance between GREX and the immune processes.

bioinformatics↗

bioRxiv2019

The properties of 5-methyltetrahydrofolate dehydrogenase (MthfD) and its role in the tetrahydrofolate (THF)-dependent dicamba demethylation system in Rhizorhabdus dicambivorans Ndbn-20

The herbicide dicamba is initially degrade via demethylation in Rhizorhabdus dicambivorans Ndbn-20. A gene cluster scaffold 66 containing a THF-dependent dicamba methyltransferase dmt and three THF metabolic-related genes, namely, mthfD, dhc and purU, is responsible for dicamba demethylation in this strain. However, the characteristics and functions of MthfD, Dhc and PurU have not been elucidated. In this study, MthfD was synthesized in Escherichia coli BL21(DE3) and purified as a His6-tagged protein. Purified MthfD was found to be a monomer, and exhibited 5-CH3-THF dehydrogenase activity in vitro. The Kcat and Km for 5-CH3-THF were 0.23 s-1 and 16.48 M, respectively. However, 5,10-CH2-THF reductase activity was not detected for MthfD yet. Gene disruption results showed that mthfD is essential for dicamba degradation, whereas dhc is dispensable. Our studies revealed that MthfD physiologically is a 5-CH3-THF dehydrogenase that catalyzes the irreversible dehydrogenation of 5-CH3-THF to 5,10-CH2-THF in the THF regeneration pathway during dicamba demethylation in R. dicambivorans Ndbn-20.

microbiology↗

bioRxiv2019

The Metabolites NADP+ and NADPH are the Targets of the Circadian Protein Nocturnin (Curled)

Nocturnin (NOCT) is a rhythmically expressed protein that regulates metabolism under the control of circadian clock. It has been proposed that NOCT deadenylates and regulates metabolic enzyme mRNAs. However, in contrast to other deadenylases, purified NOCT lacks the deadenylase activity. To identify the substrate of NOCT, we conducted a mass spectrometry screen and report that NOCT specifically and directly converts the dinucleotide NADP+ into NAD+ and NADPH into NADH. Further, we demonstrate that the Drosophila NOCT ortholog, Curled, has the same enzymatic activity. We obtained the 2.7 [A] crystal structure of the human NOCT*NADPH complex, which revealed that NOCT recognizes the chemically unique ribose-phosphate backbone of the metabolite, placing the 2-terminal phosphate productively for removal. We provide evidence for NOCT targeting to mitochondria and propose that NADP(H) regulation, which takes place at least in part in mitochondria, establishes the molecular link between circadian clock and metabolism.

biophysics↗

bioRxiv2019

Identification and characterization of a novel pic gene cluster responsible for picolinic acid degradation in Alcaligenes faecalis JQ135

Picolinic acid (PA) is a natural toxic pyridine derivative. Microorganisms can degrade and utilize PA for growth. However, the full metabolic pathway and its physiological and genetic foundation remain unknown. In this study, we identified the pic gene cluster responsible for the complete degradation of PA from Alcaligenes faecalis JQ135. PA was initially 6-hydroxylated into 6-hydroxypicolinic acid (6HPA) by PA dehydrogenase (PicA). 6HPA was then 3-hydroxylated by a four-component 6HPA monooxygenase (PicB) to form 3,6-dihydroxypicolinic acid (3,6DHPA), which was then converted into 2,5-dihydroxypyridine (2,5DHP) by a decarboxylase (PicC). The 2,5DHP was further degraded into fumaric acid, through PicD (2,5DHP dioxygenase), PicE (N-formylmaleamic acid deformylase), PicF (maleamic acid amidohydrolase), and PicG (maleic acid isomerase). Homologous pic gene clusters with diverse organizations were found to be widely distributed in -, {beta}-, and{gamma} -Proteobacteria. Our findings provide new insights into the microbial metabolism of environmental toxic pyridine derivatives. ImportancePicolinic acid is a common metabolite of L-tryptophan and some aromatic compounds and is an important intermediate of industrial concern. Although the microbial degradation/detoxification of picolinic acid has been studied for over 50 years, the underlying molecular mechanisms are still unknown. Here, we show the pic gene cluster responsible for the complete degradation of picolinic acid into the tricarboxylic acid cycle. This gene cluster was found to be widespread in other -, {beta}-, and{gamma} -Proteobacteria. These findings provide new perspective for understanding the mechanisms of picolinic acid biodegradation in bacteria.

microbiology↗

bioRxiv2019

A High-Throughput Screen of a Library of Therapeutics Identifies Substrates of P-glycoprotein

The ATP-binding cassette transporter P-glycoprotein (P-gp) is known to limit brain penetration of many chemotherapy drugs. Although Food and Drug Administration guidelines require that potential interactions of investigational drugs with P-gp be explored, often this information does not enter into the literature. As such, we developed a high-throughput screen (HTS) to identify substrates of P-gp from a series of chemical libraries, testing a total of 10,804 compounds, most of which have known mechanisms of action. We used the CellTiter-Glo viability assay to test library compounds against parental KB-3-1 human cervical adenocarcinoma cells and the colchicine-selected sub-line KB-8-5-11 that over-expresses P-gp. KB-8-5-11 cells were also tested in the presence of a P-gp inhibitor (tariquidar) to assess reversability of transporter-mediated resistance. Of the tested compounds, a total of 90 P-gp substrates were identified including 55 newly identified P-gp substrates. Substrates were confirmed using an orthogonal killing assay against HEK-293 cells transfected with P-gp. We confirmed that AT7159 (cyclin-dependent kinase inhibitor); AT9283, (Janus kinase 2/3 inhibitor); ispinesib (kinesin spindle protein inhibitor); gedatolisib (PKI-587, phosphoinositide 3-kinase/mammalian target of rampamycin inhibitor); GSK-690693 (AKT inhibitor); and KW-2478 (heat shock protein 90 inhibitor) were substrates, and direct ATPase stimulation was assessed. ABCG2 was also found to confer high levels of resistance to AT9283, GSK-690693 and gedatolisib, while ispinesib, AT7519 and KW-2478 were weaker substrates. Combinations of P-gp substrates and inhibitors were assessed to demonstrate on-target synergistic cell killing. This data will be of use in determining understanding how chemotherapeutic agents will cross the blood-brain barrier.

pharmacology and toxicology↗

bioRxiv2019

Data-driven robust detection of tissue/cell-specific markers

Tissue or cell subtype-specific and differentially-expressed genes (SDEGs) are defined as being differentially expressed in a particular tissue or cell subtype among multiple subtypes. Detecting SDEGs plays a critical rolse in molecularly characterizing and identifying tissue or cell subtypes, and facilitating supervised deconvolution of complex tissues. Unfortunately, classic differential analysis assumes a convenient null hypothesis and associated test statistic that is subtype-non-specific and thus, resulting in a high false positive rate and/or lower detection power with respect to particular subtypes. Here we introduce One-Versus-Everyone Fold Change (OVE-FC) test for detecting SDEGs. To assess the statistical significance of such test, we also propose the scaled test statistic OVE-sFC together with a mixture null distribution model and a tailored permutation scheme. Validated with realistic synthetic data sets on both type 1 error and detection power, OVE-FC/sFC test applied to two benchmark gene expression data sets detects many known and de novo SDEGs. Subsequent supervised deconvolution results, obtained using the SDEGs detected by OVE-FC/sFC test, showed superior performance in deconvolution accuracy when compared with popular peer methods.

bioinformatics↗

bioRxiv2019

Patterns of Treatment in Patients with Heart Failure with Preserved Ejection Fraction: the REasons for Geographic And Racial Differences in Stroke study

PurposeWe described medication use patterns among REasons for Geographic And Racial Differences in Stroke (REGARDS) participants hospitalized for heart failure with preserved ejection fraction (HFpEF) (152 hospitalizations, 101 unique individuals).\n\nMethodsMedication data were obtained from medical record review and Medicare Part D pharmacy claims. We compared discharge medication prescriptions between patients with and without chronic kidney disease (CKD), coronary heart disease (CHD), chronic obstructive pulmonary disease (COPD), and diabetes.\n\nResultsThe mean age was 74.8 years, 53.3% were black and 73.7% were female. Hypertension (97.2%), diabetes (65.1%), COPD (51.3%), CKD (41.1%) and history of CHD (60.9%) were common. On admission and discharge, respectively, beta-blockers (66.4%, 72.7%), angiotensin converting enzyme inhibitors or angiotensin receptor blockers (42.8%, 51.7%), diuretics (61.2%, 80.9%), loop diuretics (55.9%, 78.3%), calcium channel blockers (41.0%, 41.2%) and statins (44.7%, 50.3%) were commonly used. Spironolactone, digoxin, hydralazine plus isosorbide dinitrate (HISDN), isosorbide dinitrate alone and aldosterone receptor antagonists were used by <20%. For each medication, prescriptions were more common at discharge than admission. Many participants did not have Medicare claims for filled prescriptions in the year following discharge. A higher percentage of patients with versus without CKD, CHD, and diabetes had discharge prescriptions statins. Participants with CKD were also more likely to receive prescriptions for HISDN.\n\nConclusionBeta-blockers and diuretics were commonly prescribed at admission and discharge among HFpEF, but pharmacy claims for these medications within one-year were substantially less common. The comorbidities CHD, CKD, and diabetes were associated with prescriptions of statins at discharge.

epidemiology↗

bioRxiv2018

The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio

Common carp (Cyprinus carpio) is an allotetraploid Cyprinid species derived from recent whole genome duplication and provides an excellent model system for studying polyploid genome evolution in vertebrates. To explore the origins and consequences of tetraploidy in C. carpio, we generated three chromosome-level new reference genomes of C. carpio and compared them to the related diploid Cyprinid genome sequences. We identified a progenitor-like diploid Barbinae lineage by analysing the phylogenetic relationship of the homoeologous genes of C. carpio and their orthologues in closely related diploid Cyprinids. We then characterized the allotetraploid origin of C. carpio and divided its genome into two homoeologous subgenomes that are marked by a distinct genome similarity to their diploid progenitor. On the basis of the divergence rates of homoeologous genes and transposable elements in two subgenomes, we estimated that the two diploid progenitor species diverged approximately 23 million years ago (Mya) and merged to form the allotetraploid C. carpio approximately 12.4 Mya, which likely correlated with environmental upheavals caused by the extensive uplift of the Qinghai-Tibetan Plateau. No large-scale gene losses or rediploidization were observed in the two subgenomes. Instead, we found extensive homoeologous gene expression bias across twelve surveyed tissues, which indicates that subgenome B is dominant in homoeologous expression. DNA methylation analysis suggested that CG methylation in promoter regions plays an important role in altering the expression of these homoeologous genes in allotetraploid C. carpio. This study provides an essential genome resource and insights for extending further investigation on the evolutionary consequences of vertebrate polyploidy.

genomics↗

bioRxiv2018

Low-Density Lipoprotein Receptor-Mediated Lipidome-Transcriptome Reprogramming Impulses to Cisplatin Insensitivity

Platinum-based therapy remains the cornerstone for cancer patient management; however, its efficacy varies. Theis study demonstrated the differential expressions of low-density lipoprotein receptor (LDLR) in subtypes of epithelial ovarian carcinoma (EOC) determines cisplatin sensitivity. Its sensitive in serous EOCs (low LDLR), where insensitive in endometrioid and clear cell EOCs (high LDLR). Meanwhile, knocked-down or overexpressed LDLR in EOC could reversed the chemosensitivity pattern both in vitro and in vivo. Mechanistic dissection with transcriptome vs. lipidome trans-omics analyses elucidated the LDLR[->]LPC (Lyso-PhosphotidylCholine)[->]FAM83B (phospholipase-related)[->]FGFRs (cisplatin sensitivity and phospholipase-related) regulatory axis in cisplatin insensitivity. Implementing LPC-liposome encapsulated cisplatin could facilitate DNA-adduct formation via lipid droplets (LDs) delivery. Furthermore, Bioinformatics analyses found that the LDL/R[->]LD homeostasis alteration is critical for therapeutic prognosis. Lastly, using LPC-liposome-cisplatin improved cisplatin sensitivities in gastric cancer, renal cell carcinoma, hepatocellular carcinoma, cholangiocarcinoma, and pancreatic adenocarcinoma cells. In conclusion, this report discovered a LDL/R-reprogrammed transcriptome-lipidome network, by which impulses platinum insensitivity and disease outcome. The drug specific lipidome for liposome manufacture might be an efficienct pharmaceutics strategy for chemoagents.\n\nSignificanceLDLR reprograms cellular lipidome and transcriptome profiles to determines chemotherapy therapeutic efficacy. The LDLR-reduced LPC abundance disturbs phospholipids homeostasis of Lands cycle in LD, by which attenuates intracellular platinum transportation for DNA-adduct formation. Targeting LDLR-LD-lipidome with LPC-liposome-platinum could boost therapeutic efficacy for insensitivity.

cancer biology↗

bioRxiv2018

A novel structure-based control method for analyzing nonlinear dynamics in biological networks

Exploring complex biological systems requires adequate knowledge of the systems underlying wiring diagram but not its specific functional forms. Thus, exploration actually requires the concepts and approaches delivered by structure-based network control, which investigates the controllability of complex networks through a minimum set of input nodes. Traditional structure-based control methods focus on the structure of complex systems with linear dynamics and may not match the meaning of control well in some biological systems. Here we took into consideration the nonlinear dynamics of some biological networks and formalized the nonlinear control problem of undirected dynamical networks (NCU). Then, we designed and implemented a novel and general graphic-theoretic algorithm (NCUA) from the perspective of the feedback vertex set to discover the possible minimum sets of the input nodes in controlling the network state. We applied our NCUA to both synthetic networks and real-world networks to investigate how the network parameters, such as the scaling exponent and the degree heterogeneity, affect the control characteristics of networks with nonlinear dynamics. The NCUA was applied to analyze the patient-specific molecular networks corresponding to patients across multiple datasets from The Cancer Genome Atlas (TCGA), which demonstrates the advantages of the nonlinear control method to characterize and quantify the patient-state change over the other state-of-the-art linear control methods. Thus, our model opens a new way to control the undesired transition of cancer states and provides a powerful tool for theoretical research on network control, especially in biological fields.\n\nAuthor summaryComplex biological systems usually have nonlinear dynamics, such as the biological gene (protein) interaction network and gene co-expression networks. However, most of the structure-based network control methods focus on the structure of complex systems with linear dynamics. Thus, the ultimate purpose to control biological networks is still too complicated to be directly solved by such network control methods. We currently lack a framework to control the biological networks with nonlinear and undirected dynamics theoretically and computationally. Here, we discuss the concept of the nonlinear control problem of undirected dynamical networks (NCU) and present the novel graphic-theoretic algorithm from the perspective of a feedback vertex set for identifying the possible sets with minimum input nodes in controlling the networks. The NCUA searches the minimum set of input nodes to drive the network from the undesired attractor to the desired attractor, which is different from conventional linear network control, such as that found in the Maximum Matching Sets (MMS) and Minimum Dominating Sets (MDS) algorithms. In this work, we evaluated the NCUA on multiple synthetic scale-free networks and real complex networks with nonlinear dynamics and found the novel control characteristics of the undirected scale-free networks. We used the NCUA to thoroughly investigate the sample-specific networks and their nonlinear controllability corresponding to cancer samples from TCGA which are enriched with known driver genes and known drug target as controls of pathologic phenotype transitions. We found that our NCUA control method has a better predicted performance for indicating and quantifying the patient biological system changes than that of the state-of-the-art linear control methods. Our approach provides a powerful tool for theoretical research on network control, especially in a range of biological fields.

systems biology↗

bioRxiv2018

Immunomodulatory activity of Ganoderma lucidum immunomodulatory protein via PI3K/Akt and MAPK signaling pathways in macrophage RAW264.7 cells

Ganoderma lucidum, a traditional edible and medicinal fungus, holds an important status in health care systems in China and other Asian countries. Fungal immunomodulatory protein (FIP), one of the active ingredients isolated from G. lucidum, is a class of naturally occurring proteins and possesses potential biological functions. This study was conducted to explore the molecular mechanism of its immunomodulatory potency in immune responses of macrophages. In vitro assays of biological activity indicated that rFIP-glu significantly activated macrophage RAW264.7 cells, and possessed the ability of pro-and anti-inflammation the cells. RNA sequencing analysis showed that macrophage activation involved Toll-like receptors and mitogen-activated protein kinases pathways. Furthermore, qRT-PCR indicated that phosphoinositide 3 kinase inhibitor LY294002 blocked the mRNA levels of MCP-1, MEK1/2 inhibitor U0126 reduced the mRNA levels of TNF- and MCP-1, and JNK inhibitor SP600125 prevented the up-regulation of iNOS mRNA in the rFIP-glu-induced cells. FIP-glu mediated these inflammatory effects not through a general pathway, instead through a different pathway for different inflammatory mediator. These data indicate the possibility that rFIP-glu has an important immune-regulation function and thus has potential therapeutic uses.

immunology↗

bioRxiv2018

Robust Antibacterial Activity of Tungsten Oxide (WO3-X) Nanodots

Antibacterial agents are an important tool in the prevention of bacterial infections. Inorganic materials are attractive due to their high stability under a variety of conditions compared to organic antibacterial agents. Herein tungsten oxide nanodots (WO3-X), synthesized by a simple one-pot synthetic approach, was found to exhibit efficient antibacterial capabilities. The analyses with colony-forming units (CFU) showed excellent antibacterial activity of WO3-X against both gram-negative E. coli (Escherichia coli) and gram-positive S. aureus (Staphylococcus aureus) strains. The scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images revealed clear damage to the bacterial cell membranes, which was further confirmed by molecular dynamics simulations. Additionally, exposure to simulated sunlight was found to further increase germicidal activity of WO3-X nanodots - a 30-minute exposure to sunlight (combining 50 g/mL WO3-X nanodots) showed a 70% decrease in E. coli viability compared to without exposure. Electron spin resonance spectroscopy (ESR) was used to elucidate the underlying mechanism of this photocatalytic activity through the generation of hydroxyl radical species. Cell counting kit-8 (CCK-8) and the live/dead assay were further employed to evaluate the cytotoxicity of WO3-X nanodots on eukaryotic cells, which demonstrated their general biocompatibility. In all, our results suggest WO3-X nanodots have considerable potential in antibacterial applications, while also being biocompatible at large.

pharmacology and toxicology↗

bioRxiv2018

Effect of soybean molasses-adsorbents on in vitro ruminal fermentation characteristics, milk production performance in lactating dairy cows

This study aimed to evaluate the in vitro fermentation characteristics of corncob powder (CRP), wheat bran (WB), rice husk (RH), defatted bran (DB) and soybean hulls (SH) when mixed with soybean molasses at a ratio of 30:100 (dry matter basis), using a batch culture incubation. During in vitro study, SH showed better fermentation characteristics (including greater maximum gas production, shorter time to achieve half of Vf, greater concentrations of acetate, propionate and total VFA, and less initial fractional rate of degradation) than other four substrates, while WB had the greatest values of DM and NDF disappearance, NH3-N and butyrate concentrations among substrates. A randomized complete block designed in vivo experiment was conducted with 24 Holstein cows (534 {+/-} 58 kg BW, 2.8 {+/-} 0.7 parity, 129 {+/-} 23 d in milk) randomly assigned to three experimental diets: Control, WB (WB adsorbed to soybean molasses replaced 150 g of corn meal per 1000 g of diet dry matter [DM]) or SH (SH adsorbed to soybean molasses replaced 100 g of wheat bran and 50 g corn meal per 1000 g of diet DM). The results indicated that cows received WB diet had greater (P<0.01) milk fat and total milk solid content than cows fed control and SH diets, and cows received WB and SH diets tended to have greater (P<0.01) milk protein content and blood glutamic-pyruvic transaminase concentration than cows fed control diet. Furtherly, cows received WB diet had greater (P<0.01) blood amylase and lactate dehydrogenase concentration than that of cows fed control diet during middle lactation.\n\nIn conclusion, dietary supplementation of molasses adsorbed by-products like WB and SH have positive effect on promoting rumen fermentation, milk quality and blood metabolism in early- and middle-lactating dairy cows. The results offered a new products and feeding way in dairy farming

animal behavior and cognition↗

bioRxiv2018

Molecular epidemiology of carbapenem-resistant Enterobacter cloacae complex infections uncovers high frequency of non-carbapenemase-producers in five tertiary care hospitals from Colombia

BackgroundInfections caused by carbapenem-resistant Enterobacter cloacae (CR-Ecl) have been increasingly reported in the clinical setting; here we describe the clinical and molecular characteristics of CR-Ecl infections in a KPC endemic region.\n\nMethodsA cross-sectional study was conducted in five tertiary-care hospitals in Medellin-Colombia. All patients infected by CR-Ecl from June-2012 to June-2014 were included. Sociodemographics and clinical information was retrieved from medical records. Antimicrobial susceptibility testing, phenotypic and molecular carbapenemase detection were performed. Analysis of hsp60 and PFGE was done in a subset of isolates.\n\nResultsOf 109 patients enrolled, 60.55% (66/109) were infected with non-carbapenemase-producing-Ecl (non-CP-Ecl). CP-Ecl patients were frequently hospitalized in the ICU (37.21% vs 12.12%) and had exposure to carbapenems (39.53% vs 15.15%) compared to non-CP-Ecl infected patients. All-cause 30-day mortality was higher in CP-Ecl than non-CP-Ecl infected patients (27.91% vs 19.70%). CP-Ecl harbored KPC-2 (83.72%) and KPC-3 (6.97%). Analysis of hsp60 showed that CP-Ecl belonged primarily to cluster-VI of Enterobacter xiangfangensis (12/34) and cluster-XI (12/34) corresponding to E. cloacae subsp. cloacae. Non-CP-Ecl isolates belonged to cluster-VII/VIII (45/54), of E. hormaechi subsp. steigerwaltii. PFGE revealed isolates in cluster VII/VIII and XI were closely related within their own clusters.\n\nConclusionsThe results revealed a high frequency of non-CP-Ecl among the CR-Ecl infections in a KPC endemic region, displaying distinct clinical and molecular characteristics in comparison to CP-Ecl. The study highlights a significant contribution of non-CP-Ecl to the prevalence of CR-Ecl. Infection control measures to curtail dissemination of CR-Ecl should not only focus on CP-Ecl but should also include non-CP-Ecl.

epidemiology↗

bioRxiv2018

The study on the mechanism of \"oil-spilling\" of wolfberry (Lycium barbarum)fruits during storage

Improper storage of wolfberry fruit is liable to soften, discoloration and adhesion, we call it \"oil-spilling\". The purpose of the study is to explore the mechanism of \"oil-spilling\" of wolfberry fruits during storage. In our study, the relationship between water content, superoxide dismutase (SOD), peroxidase (POD) activity, malondialdehyde (MDA) content and the cross section, epidermal cells of wolfberry fruit were studied during storage. Results showed that wolfberry fruits began to \"oil-spilling\" on the 20th day, and with the extension of storage time, the degree of \"oil-spilling\" gradually deepened, the content of water increased and the activity of POD decreased, and the content of MDA increased. It suggested that \"oil-spilling\" was the result of improper external storage conditions, which it could promote the increase of water content and reactive oxygen free radical of wolfberry fruit, and lead to damage of cell structure and function and lipid peroxidation of cell membrane. The results explain the mechanism of \"oil-spilling\" and provide a strong basis for the establishment of scientific storage methods of wolfberry fruit.

pharmacology and toxicology↗

bioRxiv2018

Comparative Transcriptomes Analysis of Taenia pisiformis at Different Development Stages

To understand the characteristics of the transcriptional group of Taenia pisiformis at different developmental stages, and to lay the foundation for the screening of vaccine antigens and drug target genes, the transcriptomes of adult and larva of T. pisiformis were assembled and analyzed using bioinformatic tools. A total of 36,951 unigenes with a mean length of 950bp were formed, among which 12,665, 8,188, 7,577, and 6,293 unigenes have been annotated respectively by sequence similarity analysis with four databases (NR, Swiss-Prot, KOG, and KEGG). It should be noted there are 5,662 unigenes that share good similarity with the four databases and get a relatively perfect functional annotation. Besides, a total of 10,247 differentially expressed genes were screened. To be specific, 6,910 unigenes were up-regulated in the larva stage while 3,337 were down-regulated in the adult stage. To sum up, this study sequenced and analyzed the transcriptomes of the larval and adult stages of T. pisiformis. The results of differentially expressed genes in these two stages could provide basis for functional genomics, immunology and gene expression profiles of T. pisiformis.

molecular biology↗

bioRxiv2018

Exploring differentially expressed key genes related to development of follicle by RNA-seq in Peking ducks (Anas Platyrhynchos)

Duck follicle enter different reproductive phases throughout life, and follicle gene expression patterns differ according to these phases. In particular, differentially expressed genes and related to development of follicle (mRNAs) play an important role to explore the key genes in this process; however, the expression profiles of these genes remain unclear. In this study, transcriptome sequencing was used to investigate the expression levels of duck ovarian genes, and comparative transcriptional analysis was carried out to identify differential genes, cluster them into groups and function identification. The results showed differential expression of 593 coding genes between young and laying ducks, and of 518 coding genes between laying and old ducks. In further GO analysis, 35 genes from the comparison bewtween old ducks and laying ducks have significant been changed involved in hormones related to follicle development. They include up-regulated genes StAR, CYP17, EPOX, 3{beta}-HSD, CYP1B1 CYP19A1 and down-regulated genes SR-B1 in laying ducks hormone synthesis than old ducks. Among which EPOX is a key gene for time special highly expression during egg laying stage, and other key regulatory genes highly expression showed in young and laying stage and lower expression showing with follicular development stopping. Therefore, EPOX is key regulator for duck follicle development in laying period, when its expression level decrease 98% the follicular development will stopping in duck life cycle.

developmental biology↗

bioRxiv2018

Oculomotor nerve requires an early interaction with muscle precursors for nerve guidance and branch patterning

Muscle function is dependent on innervation by the correct motor nerves. Motor nerves are composed of motor axons that extend through peripheral tissues as a compact bundle, but then diverge to create nerve branches to specific muscle targets. A transition point typically occurs as motor nerves grow near their targets, where the fasciculated nerve halts further growth, then later initiates branching to muscles. The motor nerve transition point is potentially an intermediate target acting as a guidepost to present specific cellular and molecular signals for navigation. Here we describe the navigation of the oculomotor nerve with respect to eye muscle precursor cells in mouse embryos. We found that the oculomotor nerve initially grew to the eye three days prior to the appearance of any eye muscles. The oculomotor axons spread to form a plexus within a mass of eye muscle precursors, then the nerve growth paused for more than two days. This plexus persisted during primary extraocular myogenesis, with a subsequent phase in which the nerve branched out to specific muscles. To test the functional significance of the nerve-precursor contact in the plexus, we genetically ablated muscle precursors early in nerve development, prior to nerve contact. Ablation of muscle precursors resulted in oculomotor nerve fibers failing to stop to form the plexus, but instead growing past the eye. In contrast, ablating the precursor pool at later stages, after the nerve has contacted the precursor cells, results in ectopic branching restricted near the eye. These results demonstrate that muscle precursors act as an intermediate target for nerve guidance, and are required for the oculomotor nerve to transition between nerve growth and distinct stages of terminal axon branching.

neuroscience↗